Chapter 8 — An Introduction to Metabolism

8.1 — Metabolism and Energy Transformations

Metabolism encompasses all chemical reactions within an organism, organized into metabolic pathways. These pathways are regulated by enzymes and are essential for life’s energy transformations.

• Metabolic Pathway: A sequence of enzyme-catalyzed reactions transforming a starting molecule into a product.

• Catabolic Pathways: Break down complex molecules into simpler ones, releasing energy (e.g., cellular respiration).

• Anabolic Pathways: Build complex molecules from simpler ones, requiring energy input (e.g., protein synthesis).

• Kinetic Energy: Energy of motion (e.g., moving molecules).

• Potential Energy: Stored energy due to position or structure (e.g., chemical bonds).

• Chemical Energy: A form of potential energy stored in molecular bonds.

• Open Systems: Organisms exchange energy and matter with their environment (e.g., intake of food and oxygen, release of CO2 and heat).

• First Law of Thermodynamics: Energy cannot be created or destroyed, only transformed.

• Second Law of Thermodynamics: Every energy transfer increases the entropy (disorder) of the universe.

Additional info: Entropy is a measure of energy dispersal and randomness in a system.

8.2 — Free Energy and Spontaneous Reactions

Free energy determines whether a reaction can occur spontaneously. The change in free energy (ΔG) predicts reaction spontaneity.

• Gibbs Free Energy (G): The energy in a system available to do work.

• Equation:

• Exergonic Reactions: Release free energy (ΔG < 0), spontaneous.

• Endergonic Reactions: Require energy input (ΔG > 0), nonspontaneous.

• Equilibrium: ΔG = 0; no net change occurs.

Important: Spontaneous does not mean fast; high activation energy can slow reactions.

8.3 — ATP and Cellular Work

ATP (adenosine triphosphate) is the primary energy currency of the cell, coupling energy-releasing and energy-consuming processes.

• Structure: Adenine, ribose, and three phosphate groups.

• ATP Hydrolysis:

• Energy Coupling: ATP hydrolysis drives endergonic reactions via phosphorylation (transfer of a phosphate group).

• Types of Cellular Work Powered by ATP:

  • Chemical: Synthesis of macromolecules.

  • Transport: Active transport across membranes.

  • Mechanical: Muscle contraction, movement of motor proteins.

8.4 — Enzymes and Activation Energy

Enzymes are biological catalysts that accelerate reactions by lowering activation energy without being consumed.

• Activation Energy (Ea): The energy required to initiate a reaction.

• Enzyme-Substrate Complex: Temporary association between enzyme and substrate at the active site.

• Induced Fit: The enzyme changes shape to better fit the substrate, facilitating catalysis.

• Factors Affecting Enzyme Activity:

  • Temperature (optimal range; high heat can denature enzymes)

  • pH (optimal for each enzyme)

  • Substrate concentration (saturation point)

  • Cofactors (inorganic or organic; coenzymes are organic cofactors)

• Enzyme Inhibitors:

  • Competitive: Bind active site, compete with substrate.

  • Noncompetitive: Bind elsewhere, alter enzyme shape and function.

8.5 — Regulation of Enzyme Activity

Cells regulate enzymes to control metabolic pathways and conserve resources.

• Allosteric Regulation: Regulatory molecules bind away from the active site, stabilizing active or inactive forms.

• Cooperativity: Binding of a substrate to one subunit increases affinity in others (e.g., hemoglobin and oxygen).

• Feedback Inhibition: End product of a pathway inhibits an early enzyme, preventing overproduction.

Chapter 9 — Cellular Respiration and Fermentation

9.1 — Catabolic Pathways, Redox, and Electron Carriers

Cellular respiration extracts energy from organic molecules, primarily glucose, to produce ATP through redox reactions.

• Overall Equation:

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• NAD+: Electron carrier; reduced to NADH during catabolism.

• ATP Production Mechanisms:

  • Substrate-level phosphorylation: Direct transfer of phosphate to ADP.

  • Oxidative phosphorylation: ATP synthesis powered by a proton gradient generated by the electron transport chain (ETC).

9.2 — Glycolysis

Glycolysis is the anaerobic breakdown of glucose into pyruvate, producing ATP and NADH in the cytosol.

• Phases:

  • Energy investment (uses 2 ATP)

  • Energy payoff (produces 4 ATP, 2 NADH)

• Net Products per Glucose:

  • 2 Pyruvate

  • 2 Net ATP (substrate-level phosphorylation)

  • 2 NADH

  • 0 CO2

9.3 — Pyruvate Oxidation and the Citric Acid Cycle

Pyruvate is transported into mitochondria and converted to acetyl-CoA, which enters the citric acid cycle (Krebs cycle) to complete glucose oxidation.

• Pyruvate Oxidation (per pyruvate):

  • 1 Acetyl-CoA

  • 1 NADH

  • 1 CO2

• Citric Acid Cycle (per turn):

  • 2 CO2

  • 3 NADH

  • 1 FADH2

  • 1 ATP (or GTP)

• Cycle turns twice per glucose molecule.

9.4 — Oxidative Phosphorylation and Chemiosmosis

Most ATP is generated by oxidative phosphorylation, which uses the energy from electrons transferred through the ETC to create a proton gradient for ATP synthesis.

• Electron Transport Chain (ETC): Located in the inner mitochondrial membrane; electrons from NADH and FADH2 power H+ pumping.

• Oxygen: Final electron acceptor, forming water.

• Chemiosmosis: H+ flows through ATP synthase, driving ATP production.

Additional info: The efficiency of ATP production varies due to differences in shuttle mechanisms and membrane permeability.

9.5 — Fermentation and Anaerobic Respiration

Fermentation allows glycolysis to continue in the absence of oxygen by regenerating NAD+. Anaerobic respiration uses an ETC with a final electron acceptor other than oxygen.

• Alcohol Fermentation: Pyruvate → Ethanol + CO2 (e.g., yeast).

• Lactic Acid Fermentation: Pyruvate → Lactate (e.g., muscle cells, some bacteria).

9.6 — Other Fuels and Regulation of Respiration

Cells can metabolize carbohydrates, fats, and proteins for energy. Respiration is regulated to match cellular energy needs.

• Carbohydrates: Enter glycolysis as sugars.

• Fats: Glycerol enters glycolysis; fatty acids undergo beta oxidation to acetyl-CoA.

• Proteins: Amino acids enter after deamination.

• Regulation: High ATP inhibits glycolysis (e.g., via phosphofructokinase); low ATP stimulates it.

Chapter 10 — Photosynthesis

10.1 — Photosynthesis Feeds the Biosphere

Photosynthesis is the process by which autotrophs convert light energy into chemical energy, sustaining most ecosystems.

10.2 — Chloroplasts and the Overall Process

Photosynthesis occurs in chloroplasts, primarily in leaf mesophyll cells. It consists of light reactions and the Calvin cycle.

• Key Structures:

  • Stomata: Gas exchange

  • Stroma: Calvin cycle location

  • Thylakoids: Light reactions location

  • Grana: Stacks of thylakoids

• Overall Equation:

• Light Reactions: Occur in thylakoids; produce ATP, NADPH, and O2.

• Calvin Cycle: Occurs in stroma; uses ATP and NADPH to fix CO2 into G3P.

10.3 — Light Reactions: Light, Pigments, and ATP Production

Light reactions capture solar energy and convert it into chemical energy (ATP and NADPH).

• Light: Electromagnetic energy; visible spectrum ~380–740 nm.

• Pigments:

  • Chlorophyll a: Main pigment

  • Chlorophyll b, carotenoids: Accessory pigments

• Photosystems:

  • PSII (P680): Functions first, splits water, releases O2

  • PSI (P700): Functions second, produces NADPH

• Linear Electron Flow: H2O → PSII → ETC → PSI → NADP+ → NADPH

• Cyclic Electron Flow: Uses PSI only; produces ATP but not NADPH or O2.

• Chemiosmosis: Proton gradient across thylakoid membrane drives ATP synthase (photophosphorylation).

10.4 — The Calvin Cycle

The Calvin cycle uses ATP and NADPH to fix CO2 into G3P, a carbohydrate precursor.

• Phase 1: Carbon Fixation — CO2 combines with RuBP (catalyzed by rubisco), forming 3-PGA.

• Phase 2: Reduction — ATP and NADPH convert 3-PGA to G3P.

• Phase 3: Regeneration — Most G3P is used to regenerate RuBP, enabling the cycle to continue.

• For every 3 CO2: 6 G3P formed, 1 net G3P output, 5 G3P recycled, 9 ATP and 6 NADPH consumed.

Additional info: Two net G3P molecules are needed to synthesize one glucose molecule.

Connecting All Three Chapters

• Metabolism: Energy transformations, ATP, and enzyme regulation (Chapter 8).

• Cellular Respiration: Harvests energy from organic molecules to produce ATP (Chapter 9).

• Photosynthesis: Uses light energy to build organic molecules (Chapter 10).

• Redox Carriers: NADH (respiration), NADPH (photosynthesis).

• ATP: Powers cellular work, produced by both respiration and photosynthesis.

Essential Concepts to Remember

1. Energy cannot be created or destroyed, only transformed.

2. Catabolic pathways break down molecules; anabolic pathways build molecules.

3. Exergonic reactions: ΔG < 0; Endergonic reactions: ΔG > 0.

4. Enzymes lower activation energy, not ΔG.

5. ATP couples energy-releasing and energy-requiring reactions.

6. Oxidation = loss of electrons; Reduction = gain of electrons.

7. Glycolysis: 2 pyruvate, 2 net ATP, 2 NADH per glucose.

8. Oxygen is the final electron acceptor in aerobic respiration.

9. Most ATP is made via oxidative phosphorylation.

10. Fermentation regenerates NAD+ for glycolysis.

11. Light reactions: ATP, NADPH, O2 production.

12. Calvin cycle: Uses CO2, ATP, NADPH to make G3P.

13. Photosynthesis and respiration both involve electron transfer and energy transformations.

Study Tip: For each pathway, ask: Where does it happen? What enters? What leaves? Why does the cell need it?